Get the Constituent Consortia

Returns the ConsortiumMetabolism objects that a container is built from. Defined for ConsortiumMetabolismSet (the consortia in the set) and ConsortiumMetabolismAlignment (the consortia that produced the alignment). The plural noun reflects that the result is always a collection; for a single ConsortiumMetabolism, use as.data.frame() to obtain the underlying edge list.

Usage

consortia(object)

# S4 method for class 'ConsortiumMetabolismAlignment'
consortia(object)

# S4 method for class 'ConsortiumMetabolismSet'
consortia(object)

Arguments

object

A ConsortiumMetabolismSet object.

Value

A named list of ConsortiumMetabolism objects.

Methods (by class)

• consortia(ConsortiumMetabolismAlignment): Not applicable to ConsortiumMetabolismAlignment. By design the class is a lightweight result object: it records the names of its inputs (QueryName / ReferenceName) but does not retain copies of the ConsortiumMetabolism objects themselves. Look up the originating CMs by name from the source ConsortiumMetabolismSet.

• consortia(ConsortiumMetabolismSet): Get the list of ConsortiumMetabolism objects from a ConsortiumMetabolismSet.

Examples

cm1 <- synCM("a", n_species = 3, max_met = 5)
cm2 <- synCM("b", n_species = 3, max_met = 5)
cms <- ConsortiumMetabolismSet(list(cm1, cm2), name = "demo")
#> 
#> ── Creating CMS "demo" ─────────────────────────────────────────────────────────
#> ℹ Validating 2 <ConsortiumMetabolism> objects
#> ✔ Validating 2 <ConsortiumMetabolism> objects [10ms]
#> 
#> ℹ Collecting metabolites from 2 consortia
#> ✔ Collecting metabolites from 2 consortia [28ms]
#> 
#> ℹ Re-indexing 6 unique metabolites
#> ✔ Re-indexing 6 unique metabolites [25ms]
#> 
#> ℹ Expanding 2 binary matrices to 6-dimensional space
#> ✔ Expanding 2 binary matrices to 6-dimensional space [23ms]
#> 
#> ℹ Computing 6 x 6 levels matrix
#> ✔ Computing 6 x 6 levels matrix [24ms]
#> 
#> ℹ Computing pairwise overlap (1 pairs via crossprod)
#> ✔ Computing pairwise overlap (1 pairs via crossprod) [22ms]
#> 
#> ℹ Assembling pathway data from 2 consortia
#> ✔ Assembling pathway data from 2 consortia [29ms]
#> 
#> ℹ Building dendrogram from 2 x 2 dissimilarity matrix
#> ✔ Building dendrogram from 2 x 2 dissimilarity matrix [21ms]
#> 
#> ℹ Extracting dendrogram node positions
#> ✔ Extracting dendrogram node positions [23ms]
#> 
#> ℹ Collecting 2 consortium graphs
#> CMS "demo" created: 2 consortia, 6 metabolites (0.2s)
#> ✔ Collecting 2 consortium graphs [86ms]
#> 
consortia(cms)
#> [[1]]
#> 
#> ── ConsortiumMetabolism 
#> Name: "a"
#> Weighted metabolic network: 3 species, 3 metabolites, 3 pathways.
#> Pathways per species: min 1, mean 1.3, max 2.
#> 
#> [[2]]
#> 
#> ── ConsortiumMetabolism 
#> Name: "b"
#> Weighted metabolic network: 3 species, 5 metabolites, 10 pathways.
#> Pathways per species: min 1, mean 3.7, max 6.
#>